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Sample GSM3691936 Query DataSets for GSM3691936
Status Public on Jun 11, 2021
Title Activated_DNT_1
Sample type SRA
 
Source name spleen T cells of eight-week-old C57BL/6 male mice
Organism Mus musculus
Characteristics cell type: TCRalphabeta + T cells
cell subset: Activated_DN
strain: C57BL/6
tissue: spleen
Sex: male
Extracted molecule polyA RNA
Extraction protocol cDNA libraries were obtained using Chromium Single Cell 3’ Library & Gel Bead Kit v2
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description We stimulated the naïve DNT cells with anti-CD3/CD28 antibody and 20 ng/ml IL-2 for 3 days in vitro to obtain the activated DNT cells.
Data processing For TCRab_Tcell, naïve_DNT_1, activated_DNT_1, CD4_Tcell and CD8_Tcell samples, 10x Genomics cellranger mkfastq (version 2.1.0) was used to demultiplex raw base call (BCL) files generated by Illumina sequencers into FASTQ files. For Naïve_DNT_2 and activated_DNT_2 samples, 10x Genomics cellranger mkfastq (version 3.1.0) was used to demultiplex raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
R1 = 16bp cell barcode + 10bp UMI barcode. R2 = biological
For TCRab_Tcell, naïve_DNT_1, activated_DNT_1, CD4_Tcell and CD8_Tcell samples, cellranger count (version 2.1.0) aligns the fastq files to the mm10 genome, filter and count the barcode and UMIs. For Naïve_DNT_2 and activated_DNT_2 samples, cellranger count (version 3.0.1) aligns the fastq files to the mm10 genome, filter and count the barcode and UMIs.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Row information of gene name is in genes.tsv. Column information of cell barcodes is in barcodes.tsv. Matrix file of read counts is in matrix.mtx.
 
Submission date Mar 29, 2019
Last update date Jun 15, 2021
Contact name YangLu Yang
E-mail(s) lucyyang1991@hotmail.com
Organization name Beijing Friendship Hospital, Capital Medical University
Street address Beijing Xicheng District Yongan Road NO.95
City Beijing
State/province Beijing
ZIP/Postal code 100053
Country China
 
Platform ID GPL21273
Series (1)
GSE129030 Transcriptome landscape of double negative T cells by single-cell RNA sequencing
Relations
BioSample SAMN11285854
SRA SRX5599401

Supplementary file Size Download File type/resource
GSM3691936_Activated_DNT_1_barcodes.tsv.gz 8.2 Kb (ftp)(http) TSV
GSM3691936_Activated_DNT_1_genes.tsv.gz 212.7 Kb (ftp)(http) TSV
GSM3691936_Activated_DNT_1_matrix.mtx.gz 16.9 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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